REL: 2.3.0

[effigies]

Open issues/PRs that could go in quickly

• ENH: Add image slicing #550 [PR] (Submitter: @effigies; Reviewer: @matthew-brett)
• NF: Functionality for reading AFNI BRIK/HEAD #561 [PR] (Submitter: @rmarkello; Reviewer: @matthew-brett)
• ENH: adding TRK <=> TCK streamlines conversion scripts #606 [PR] (Submitter: @MarcCote)
• ENH: Take advantage of IndexedGzipFile drop_handles flag #614 [PR] (Submitter: @pauldmccarthy; Reviewer: @effigies @matthew-brett)
• RF: moving more cmdline things to the cmdline folder #615 [PR] (Submitter: @chrispycheng; Reviewer: @yarikoptic)
• NF nib-diff #617 [PR] (Submitter: @chrispycheng; Reviewer: @yarikoptic)
• BUG?: MGHHeader.set_zooms() does not persist on I/O roundtrip or affect affine #619 [BUG] (Submitter: @larsoner)

Pre-release checklist

• Review the open list of nibabel issues. Check whether there are outstanding issues that can be closed, and whether there are any issues that should delay the release. Label them!
• Review and update the release notes. Review and update the Changelog file.
• Look at doc/source/index.rst and add any authors not yet acknowledged.
• Use the opportunity to update the .mailmap file if there are any duplicate authors listed from git shortlog -nse.
• Check the copyright year in doc/source/conf.py
• Refresh the README.rst text from the LONG_DESCRIPTION in info.py by running make refresh-readme.
• Check the dependencies listed in nibabel/info.py (e.g. NUMPY_MIN_VERSION) and in doc/source/installation.rst and in requirements.txt and .travis.yml. They should at least match. Do they still hold? Make sure nibabel on travis is testing the minimum dependencies specifically.
• nibabel-release-checks
  • make sdist-tests errors
  • make check-version-info
  • make check-files
  • make -C doc doctest
  • python -m compileall .
  • make source-release
• Make sure all tests pass (from the nibabel root directory): nosetests --with-doctest nibabel
• Edit nibabel/info.py to set _version_extra to ''; commit
• Build bots
  • nibabel-py2.7-osx-10.10
  • nibabel-bdist32-27
  • nibabel-bdist32-33
  • nibabel-bdist32-34
  • nibabel-bdist32-35
  • nibabel-bdist64-27 [buildslave offline]

Adapted from http://nipy.org/nibabel/devel/make_release.html#release-checklist

Closes #622
Closes #631

[codecov-io]

Codecov Report

Merging #632 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master     #632   +/-   ##
=======================================
  Coverage   88.81%   88.81%           
=======================================
  Files          92       92           
  Lines       11278    11278           
  Branches     1848     1848           
=======================================
  Hits        10017    10017           
  Misses        926      926           
  Partials      335      335

Impacted Files	Coverage Δ
nibabel/info.py	100% <100%> (ø)	⬆️

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[coveralls]

Coverage remained the same at 91.789% when pulling 12da3be on rel/2.3.0 into 0045ed4 on master.

[pauldmccarthy]

Hey @effigies and @matthew-brett , I will try and finish off #614 over the next week.

[effigies]

@pauldmccarthy For the sake of having enough time to properly test and release before OHBM, I would like to avoid merging anything for 2.3.0 after tomorrow.

Finishing this off soon would obviously be welcome, and I would support a micro-release once it is in, as I think deprecating that API sooner than later would be a good move. Just wanted to comment, to calibrate your expectations, here.

[effigies]

Also, part of the short turnaround here has to do with the holiday this past Monday. I was mentally in Tuesday, yesterday, so I didn't realize I was giving only 2 days warning.

[pauldmccarthy]

@effigies Ok ... I have just moved house (relocated across the country), but will do my best to get it in a mergable state over the next couple of days!

[effigies]

@matthew-brett There seem to be issues with the nibabel-py2.7-osx-10.10 and nibabel-bdist64-27 buildbots. On the former, pip has been failing since Mar 29. On the latter, the buildslave has been down since at least Apr 13.

[matthew-brett]

Sorry about the buildbots - I'm not in that office any more so it's harder to maintain them.

I fixed the OSX build. I'll ask someone to reboot the Windows machine that appears to be down.

[yarikoptic]

I would really love to see #615 merged since it is the right thing to do ;-) BUT I've stumbled on difficulty to make doctests to not crash while trying to import that fuse-based dicomfs submodule which wouldn't be present on some systems... any hints would be super useful

[nibotmi]

☔ The latest upstream changes (presumably #550) made this pull request unmergeable. Please resolve the merge conflicts.

[yarikoptic]

@effigies tested a few reverse depends on stretch (on sid - there are issues we need to fix in them) -- all good. The only one is dcmstack for which we fixed the issue in nibabel for deterministic slice order magic -- yet to upload fresh release (0.7.0) so could be ignored I think (alternatively, I could test again or fix up later)

neurodebian@smaug ..uilds/nibabel/2.3.0+git432-g58418066-1 % cat nibabel_2.3.0+git432-g58418066-1~nd90+1_amd64.testrdepends.nd+debian-stretch.summary

Testing builds against nibabel_2.3.0+git432-g58418066-1~nd90+1.dsc
cfflib_2.0.5-2.dsc                                 ok      ok
dcmstack_0.6.2+git33-gb43919a.1-1.dsc              ok   FAILED /home/neurodebian/deb/builds/nibabel/2.3.0+git432-g58418066-1/nibabel_2.3.0+git432-g58418066-1~nd90+1_amd64.testrdepends.nd+debian-stretch/srcs/new/dcmstack_0.6.2+git33-gb43919a.1-1_amd64.build
nitime_0.7-1.dsc                                   ok      ok
pymvpa2_2.6.0-1.dsc                                ok      ok
pysurfer_0.7-2.1~deb9u1.dsc                        ok      ok